Clonal diversity of Streptococcus pneumoniae serotype 19A collected from children < 5 years old in Quebec, Canada, 2016-2021

Streptococcus pneumoniae serotype 19A is a highly diverse, often antimicrobial-resistant Gram-positive bacterium which can cause invasive pneumococcal disease (IPD). In 2021, public health authorities in the Canadian province of Qu & eacute;bec observed an increase of serotype 19A IPD in children <5 years. The purpose of this study was to determine the clonal composition of serotype 19A isolates collected from this age group in Qu & eacute;bec, from 2016 to 2021. Forty-one and 37 IPD isolates from children <5 years from Qu & eacute;bec and the remainder of Canada, respectively, were sequenced using the Illumina NextSeq platform. Phylogenetic analysis using SNVPhyl identified three clusters, corresponding to three common clones of serotype 19A: CC199, CC320 and ST695. CC199, predominantly represented by ST416, accounted for similar proportions of serotype 19A isolates collected from children in Qu & eacute;bec (19.5 %) and other Canadian jurisdictions (OCJs, 21.6 %), with significant presence of ermB (62.5 % and 60 % of ST416 isolates, respectively). CC320 was more commonly identified from OCJs in comparison to Qu & eacute;bec (18.9 % vs. 7.3 %, respectively), but were highly antimicrobial-resistant regardless of region. ST695 was the most common clone of serotype 19A collected in Qu & eacute;bec from children <5 years, representing 65.9 % of isolates collected over the study period (40.5 % of isolates collected in OCJs). Phylogenetic analysis identified geographical differences in ST695 across Canada; including a large clade specific to Qu & eacute;bec (with both susceptible and macrolide-resistant [ermB] subclades), and a separate macrolide-resistant (mefA) clade associated with OCJs. The Qu & eacute;bec-specific ermB-ST695 clone represented 48.1 % of ST695 collected from the province. Continued genomic surveillance of S. pneumoniae serotype 19A is required to: i) track the prevalence and clonal composition of serotype 19A in Qu & eacute;bec in future years; ii) characterize the clonal distribution of serotype 19A in adult populations; and iii) monitor whether the currently geographically restricted ermB-ST695 clone observed in Qu & eacute;bec expands to OCJs.

Automated summary

This study aimed to determine the clonal composition of serotype 19A isolates collected from children <5 years in the Canadian province of Québec from 2016 to 2021. The results showed three common clones of serotype 19A: CC199, CC320, and ST695. ST695 was the most common clone collected in Québec, while CC320 was more common in other Canadian jurisdictions. Continued genomic surveillance is important to track the prevalence and clonal distribution of serotype 19A in Québec and to monitor its spread to other regions.